John Bogovic bogovicj

Deformable 2D and 3D big data image registration and transformation with BigWarp

I2K 2024 From Images to Knowledge
Milan, Italy
Oct 24, 2024 9:45 AM

BigWarp is an intuitive tool for non-linear manual image registration that can scale to terabyte-sized image data. In this


	n5 = new N5Factory().openReader("/home/john/tmp/mitosis.zarr");
	println(n5.getClass());

	node = N5DatasetDiscoverer.discover(n5);
	println(node.printRecursive());
	println(node.getDescendant("s0").get().getMetadata().getClass());

	import org.janelia.saalfeldlab.n5.N5Reader;
	import org.janelia.saalfeldlab.n5.ij.N5Importer;


	n5 = new N5Factory().openReader("/home/john/tmp/mitosis.zarr");
	println(n5.getClass());

	node = N5DatasetDiscoverer.discover(n5);
	println(node.printRecursive());
	println(node.getDescendant("s0").get().getMetadata().getClass());

	import org.janelia.saalfeldlab.n5.N5Reader;
	import org.janelia.saalfeldlab.n5.ij.N5Importer;

	#!/bin/bash

	function initialize() {

	# Make sure the guard is oriented to the right
	#
	# I happen to know that the guard is oriented up for my input
	# So the commands below do a clock-wise rotation
	# (this would be easy enough to generalize)

	/**
	* Reads a {@link DataBlock} from an {@link InputStream}.
	*
	* @param in
	* @param datasetAttributes
	* @param gridPosition
	* @return
	* @throws IOException
	*/
	@SuppressWarnings("incomplete-switch")


	public T getValidateDefault(String parameter, Predicate<T> validator, T defaultValue) {
	return getOptional(parameter).filter(validator)
	.map(x -> {
	allDefault = false;
	return x;
	}).orElse(defaultValue);
	}

	#@ File(styles="both") root
	#@ String(value="/") datasetPath

	/*
	* If you used Fiji to export a multi-scale image with N5Viewer metadata using average downsampling
	* between approximately March 13 and April 15 2024, the translation metadata may be incorrect.
	*
	* Running this script will correct the metadata.
	*
	* John Bogovic